The destruction had nothing to do with 9/11. It was all about CYA. Identifying US persons as possible terrorists by the military would have placed a very bright spotlight on our intelligence gathering agencies and methods.
The destruction was probably ordered to get rid of the evidence that could be used (ACLU?) to show attempts were made to identify these suspects to the agency (FBI) legally responsible for conducting surveillance of persons within this country.
You need to read this if you haven't already:
MILITARY 'SPIED' ON RICE (More Able Danger leaks from Specter staffers)
The private contractors working for the counter-terrorism unit Able Danger lost their jobs in May 2000. The firings following a series of analyses that Pentagon lawyers feared were dangerously close to violating laws banning the military from spying on Americans, sources said.
The Pentagon canceled its contract with the private firm shortly after the analysts who were working on identifying al Qaeda operatives produced a particularly controversial chart on proliferation of sensitive technology to China, the sources said.
Sources said the private contractors, using sophisticated computer software that sifts through massive amounts of raw data to establish patterns, came up with a chart of Chinese strategic and business connections in the U.S.
There is one account of a big (internal) fuss about ABLE DANGER in May 2000 (during Clinton administration) when the private contractor doing at least a key segment of the work was abruptly fired (see below). But I have the strong impression that AD was not terminated as a program until Feb. 2001 -- I'll try to find the link for that, it's somewhere on the 'ATTA' list of threads.